The moves tracked broader weakness in commodity markets, as the 19-commodity Thomson Reuters Core Commodity Index touched its weakest levels in over a week.
May New York cocoa settled down $26, or 1.1 percent, at $2,254 per tonne, largely erasing gains made the previous session, when the contract touched a one-week high.
The market was back on the defensive after a short-covering rally since the start of the month ran out of steam, dealers said.
Total open interest fell over the course of that rally to reach 244,865 lots on Wednesday, its lowest level in over a month, ICE data showed.
The market has been weighed by plentiful supplies out of West Africa.
Cocoa arrivals at ports in second-largest producer Ghana reached 618,520 tonnes between the start of this year's harvest on Oct. 1 and Jan. 24, up 11 percent year-on-year, data from the marketing board showed.
May London cocoa settled down 17 pounds, or 1 percent, at 1,670 pounds per tonne.
March raw sugar settled down 0.17 cent, or 1.3 percent, at 12.73 cents per lb, erasing Wednesday's gains.
Prices were pressured by weakness in oil markets. Lower oil prices can diminish the competitiveness of cane-derived ethanol in Brazil, raising the possibility of mills increasing the amount of cane used to make sugar.
March white sugar settled down $3.70, or 1.1 percent, at $337.70 per tonne.
March arabica coffee settled down 1.2 cent, or 1.1 percent, at $1.043 per lb.
Prices have been pressured by the diminishing threat of dry weather in top grower Brazil, dealers said. March robusta coffee settled down $9, or 0.6 percent, at $1,547 per tonne.